Research article
Word correlation matrices for protein sequence analysis and remote homology detection
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* Corresponding author: Thomas Lingner thomas@gobics.de
Department of Bioinformatics, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Göttingen, Germany
BMC Bioinformatics 2008, 9:259 doi:10.1186/1471-2105-9-259
Published: 3 June 2008Abstract
Background
Classification of protein sequences is a central problem in computational biology. Currently, among computational methods discriminative kernel-based approaches provide the most accurate results. However, kernel-based methods often lack an interpretable model for analysis of discriminative sequence features, and predictions on new sequences usually are computationally expensive.
Results
In this work we present a novel kernel for protein sequences based on average word similarity between two sequences. We show that this kernel gives rise to a feature space that allows analysis of discriminative features and fast classification of new sequences. We demonstrate the performance of our approach on a widely-used benchmark setup for protein remote homology detection.
Conclusion
Our word correlation approach provides highly competitive performance as compared with state-of-the-art methods for protein remote homology detection. The learned model is interpretable in terms of biologically meaningful features. In particular, analysis of discriminative words allows the identification of characteristic regions in biological sequences. Because of its high computational efficiency, our method can be applied to ranking of potential homologs in large databases.